Julio Saez-Rodriguez

According to our database1, Julio Saez-Rodriguez authored at least 59 papers between 2001 and 2021.

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Bibliography

2021
FUNKI: Interactive functional footprint-based analysis of omics data.
CoRR, 2021

A comprehensive database for integrated analysis of omics data in autoimmune diseases.
BMC Bioinform., 2021

The Minimum Information about a Molecular Interaction CAusal STatement (MI2CAST).
Bioinform., 2021

Setting the basis of best practices and standards for curation and annotation of logical models in biology - highlights of the [BC]2 2019 CoLoMoTo/SysMod Workshop.
Briefings Bioinform., 2021

Reusability and composability in process description maps: RAS-RAF-MEK-ERK signalling.
Briefings Bioinform., 2021

2020
BIAS: Transparent reporting of biomedical image analysis challenges.
Medical Image Anal., 2020

Converting networks to predictive logic models from perturbation signalling data with CellNOpt.
Bioinform., 2020

Bringing data from curated pathway resources to Cytoscape with OmniPath.
Bioinform., 2020

2019
Hybrid parallel multimethod hyperheuristic for mixed-integer dynamic optimization problems in computational systems biology.
J. Supercomput., 2019

Towards Explainable Anticancer Compound Sensitivity Prediction via Multimodal Attention-based Convolutional Encoders.
CoRR, 2019

2018
Computational discovery of dynamic cell line specific Boolean networks from multiplex time-course data.
PLoS Comput. Biol., 2018

A systematic atlas of chaperome deregulation topologies across the human cancer landscape.
PLoS Comput. Biol., 2018

PaccMann: Prediction of anticancer compound sensitivity with multi-modal attention-based neural networks.
CoRR, 2018

GDSCTools for mining pharmacogenomic interactions in cancer.
Bioinform., 2018

2017
Data-driven reverse engineering of signaling pathways using ensembles of dynamic models.
PLoS Comput. Biol., 2017

Systematic Analysis of Transcriptional and Post-transcriptional Regulation of Metabolism in Yeast.
PLoS Comput. Biol., 2017

caspo: a toolbox for automated reasoning on the response of logical signaling networks families.
Bioinform., 2017

Benchmarking substrate-based kinase activity inference using phosphoproteomic data.
Bioinform., 2017

2016
A computational method for designing diverse linear epitopes including citrullinated peptides with desired binding affinities to intravenous immunoglobulin.
BMC Bioinform., 2016

Efficient randomization of biological networks while preserving functional characterization of individual nodes.
BMC Bioinform., 2016

2015
Learning Boolean logic models of signaling networks with ASP.
Theor. Comput. Sci., 2015

BioPreDyn-bench: a suite of benchmark problems for dynamic modelling in systems biology.
BMC Syst. Biol., 2015

Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies.
BMC Bioinform., 2015

Cooperative development of logical modelling standards and tools with CoLoMoTo.
Bioinform., 2015

Reverse engineering of logic-based differential equation models using a mixed-integer dynamic optimization approach.
Bioinform., 2015

2014
BioPreDyn-bench: benchmark problems for kinetic modelling in systems biology.
CoRR, 2014

Using Python to Dive into Signalling Data with CellNOpt and BioServices.
CoRR, 2014

Network topology and parameter estimation: from experimental design methods to gene regulatory network kinetics using a community based approach.
BMC Syst. Biol., 2014

MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.
BMC Bioinform., 2014

A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models.
Biosyst., 2014

Fast randomization of large genomic datasets while preserving alteration counts.
Bioinform., 2014

2013
MEIGO: an open-source software suite based on metaheuristics for global optimization in systems biology and bioinformatics.
CoRR, 2013

Network based elucidation of drug response: from modulators to targets.
BMC Syst. Biol., 2013

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.
BMC Syst. Biol., 2013

Path2Models: large-scale generation of computational models from biochemical pathway maps.
BMC Syst. Biol., 2013

CySBGN: A Cytoscape plug-in to integrate SBGN maps.
BMC Bioinform., 2013

DvD: An R/Cytoscape pipeline for drug repurposing using public repositories of gene expression data.
Bioinform., 2013

Exhaustively characterizing feasible logic models of a signaling network using Answer Set Programming.
Bioinform., 2013

BioServices: a common Python package to access biological Web Services programmatically.
Bioinform., 2013

2012
Machine learning prediction of cancer cell sensitivity to drugs based on genomic and chemical properties
CoRR, 2012

Revisiting the Training of Logic Models of Protein Signaling Networks with a Formal Approach based on Answer Set Programming
CoRR, 2012

CellNOptR: a flexible toolkit to train protein signaling networks to data using multiple logic formalisms.
BMC Syst. Biol., 2012

Creating and analyzing pathway and protein interaction compendia for modelling signal transduction networks.
BMC Syst. Biol., 2012

Integrating literature-constrained and data-driven inference of signalling networks.
Bioinform., 2012

Revisiting the Training of Logic Models of Protein Signaling Networks with ASP.
Proceedings of the Computational Methods in Systems Biology, 2012

2011
Training Signaling Pathway Maps to Biochemical Data with Constrained Fuzzy Logic: Quantitative Analysis of Liver Cell Responses to Inflammatory Stimuli.
PLoS Comput. Biol., 2011

2009
The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data.
PLoS Comput. Biol., 2009

Identifying Drug Effects via Pathway Alterations using an Integer Linear Programming Optimization Formulation on Phosphoproteomic Data.
PLoS Comput. Biol., 2009

Fuzzy Logic Analysis of Kinase Pathway Crosstalk in TNF/EGF/Insulin-Induced Signaling.
PLoS Comput. Biol., 2009

Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling.
BMC Syst. Biol., 2009

2008
Flexible informatics for linking experimental data to mathematical models via <i>DataRail</i>.
Bioinform., 2008

Automatic decomposition of kinetic models of signaling networks minimizing the retroactivity among modules.
Proceedings of the ECCB'08 Proceedings, 2008

2007
A Logical Model Provides Insights into T Cell Receptor Signaling.
PLoS Comput. Biol., 2007

Structural and functional analysis of cellular networks with CellNetAnalyzer.
BMC Syst. Biol., 2007

2006
Visual setup of logical models of signaling and regulatory networks with ProMoT.
BMC Bioinform., 2006

A methodology for the structural and functional analysis of signaling and regulatory networks.
BMC Bioinform., 2006

A domain-oriented approach to the reduction of combinatorial complexity in signal transduction networks.
BMC Bioinform., 2006

2005
Dissecting the puzzle of life: modularization of signal transduction networks.
Comput. Chem. Eng., 2005

2001
Topological Analysis and Visualisation of large Signalling Networks: The TGF-beta Signal Transductionin Eukaryotic Systems.
Proceedings of the Computer science and biology: Proceedings of the German Conference on Bioinformatics, 2001


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